Recon3D enables a three-dimensional view of gene variation in human metabolism
Artikel i vetenskaplig tidskrift, 2018

Genome-scale network reconstructions have helped uncover the molecular basis of metabolism. Here we present Recon3D, a computational resource that includes three-dimensional (3D) metabolite and protein structure data and enables integrated analyses of metabolic functions in humans. We use Recon3D to functionally characterize mutations associated with disease, and identify metabolic response signatures that are caused by exposure to certain drugs. Recon3D represents the most comprehensive human metabolic network model to date, accounting for 3,288 open reading frames (representing 17% of functionally annotated human genes), 13,543 metabolic reactions involving 4,140 unique metabolites, and 12,890 protein structures. These data provide a unique resource for investigating molecular mechanisms of human metabolism. Recon3D is available at http://vmh.life.

Författare

Elizabeth Brunk

University of California

Danmarks Tekniske Universitet (DTU)

S. Sahoo

Université du Luxembourg

Daniel C. Zielinski

University of California

Ali Altunkaya

Arizona State University

San Diego Supercomputer Center

Andreas Dräger

Universität Tübingen

Nathan Mih

University of California

Francesco Gatto

University of California

Chalmers, Biologi och bioteknik, Systembiologi

Avlant Nilsson

Chalmers, Biologi och bioteknik, Systembiologi

German Andres Preciat Gonzalez

Université du Luxembourg

M. K. Aurich

Université du Luxembourg

Andreas Prlic

San Diego Supercomputer Center

Anand Sastry

University of California

Anna D. Danielsdottir

Université du Luxembourg

Almut Heinken

Université du Luxembourg

Alberto Noronha

Université du Luxembourg

Peter W. Rose

San Diego Supercomputer Center

Stephen K. Burley

San Diego Supercomputer Center

Rutgers Cancer Institute of New Jersey

R. M. T. Fleming

Universiteit Leiden

Université du Luxembourg

Jens Christian Froslev Nielsen

Chalmers, Biologi och bioteknik, Systembiologi

Danmarks Tekniske Universitet (DTU)

I. Thiele

Université du Luxembourg

B. O. Palsson

Danmarks Tekniske Universitet (DTU)

University of California

Nature Biotechnology

1087-0156 (ISSN)

Vol. 36 3 272-281

Ämneskategorier

Biokemi och molekylärbiologi

Bioinformatik (beräkningsbiologi)

Bioinformatik och systembiologi

DOI

10.1038/nbt.4072

Mer information

Senast uppdaterat

2018-04-04